Showing : ChiPseeker • reset
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Chip Seq Analysis of RNA Polymerase 2
ChIPseeker ChIPSeqData ChIPSeq Bioconductor
written 27 days ago by • 0
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619
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ChIPseeker peak_Profile_Heatmap color palette
ChIPseeker
21 months ago Anton01 • 0
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0
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692
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[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
22 months ago Henry ▴ 10
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1
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823
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plotAvgProf - How to change labels in the facet option
ChIPseeker
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
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2
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1.8k
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annotatePeak error for some problem
ChIPseeker
written 2.3 years ago by • 0
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2
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2.0k
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how i can get the name of genes in pathway?
chipseq ChIPseeker
3.0 years ago chavaleab • 0
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1.1k
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Can ChiPseeker be as highly customizable as "computeMatrix"? for example if I want to plot the distribution of genes on the TAD boundary?
deeptools ChIPseeker
3.0 years ago 840842906 • 0
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1
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1.7k
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Create an Annotation DB file for a non-model organism
AnnotationDbi annotation ChIPseeker
updated 3.1 years ago by 68k • written 3.1 years ago by ▴ 50
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2
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7.1k
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Cannot install packages in R/BiocManager_Warning message: package(s) not installed when version(s) same as or greater than current; use `force = TR…
Bioconductor BioCManager ChIPseeker
updated 3.2 years ago by 68k • written 3.2 years ago by • 0
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1.2k
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Statistical test for genomic annotation by ChIPseeker
statistics PeakAnnotation ChIPseeker GuangchuangYu
3.6 years ago arisarkar88 ▴ 40
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0
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1.5k
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Problem with "TxDb.Mmusculus.UCSC.mm39.refGene" to annotate genes with ChIPseeker
TxDb.Mmusculus.UCSC.mm39.refGene ChIPseeker annotate
3.7 years ago Palmira • 0
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0
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3.9k
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How to define 'distal intergenic'
ChIPseeker
3.7 years ago Sanghoon • 0
0
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1
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1.8k
views
ChIP-seq peak annotation to gene in ChIPseeker
ChIPseeker
3.8 years ago Gyan Prakash Mishra ▴ 10
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0
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1.2k
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Can we get an Average Profile of ChIP peaks binding to Transcription "START and STOP site" both in a single plot?
ChIPSeq ChIPseeker
3.8 years ago Swadha • 0
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1.2k
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What is weightcol doing in getTagMatrix() function of ChIPseeker?
ChIPseeker
3.9 years ago hyjforesight • 0
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1
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2.5k
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ChIPseeker issue with plotpeakProf2 when making plot of peak profile across gene body and flanks
ChIPseeker
4.3 years ago william.ho • 0
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2
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1.7k
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getPromoters
ChIPseeker
4.4 years ago guoyou88 • 0
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0
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1.2k
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ChIPseeker, how to customize plotDistToTSS
ChIPseeker
4.4 years ago alexandre.blais ▴ 50
1
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3
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1.5k
views
what does " * " denote under the strand column of the GRanges object file output
ChIPseeker
4.7 years ago Meghna • 0
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0
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1.4k
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CHIPseeker- promoter gene names
ChIPseeker CHIPsee
4.8 years ago rb • 0
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1
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2.5k
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ChIPseeker: Annotating Peaks with both upstream and downstream gene
ChIPseeker
updated 4.9 years ago by ▴ 10 • written 4.9 years ago by ▴ 10
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0
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1.4k
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What is the definition of flank_gene_distances output field in ChIPseeker
ChIPseeker
4.9 years ago Sam ▴ 10
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0
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1.6k
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Annotation of downstream in ChIPseeker
downstream Priority ChIPseeker
4.9 years ago Xiaojie Cheng • 0
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2
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1.6k
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ChIPseeker failing on r-devel on CRAN checks
ChIPseeker cinaR
5.0 years ago • updated 4.9 years ago Onur Karakaslar • 0
1
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4
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3.5k
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Genome annotation file in TxDb.Mmusculus.UCSC.mm10.knownGene
ChIPseeker TxDb.Mmusculus.UCSC.mm10.knownGene
5.0 years ago Kasit • 0
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0
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1.2k
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ChIPSeeker covplot function, fix yaxis
ChIPseeker
5.1 years ago jordi.planells • 0
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0
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1.3k
views
Genes in ChIPseeker annotation do not exist in the organism
ChIPseeker
5.3 years ago • updated 5.2 years ago Sam ▴ 10
2
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2
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3.2k
views
ChIP seeker annotation error
DiffBind chipseq ChIPseeker ChipDb annotation
5.3 years ago • updated 5.1 years ago Mar Mar ▴ 20
5
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3
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3.1k
views
importing BED with non-integer values
ChIPseeker ChIPSeqData
updated 5.3 years ago by 68k • written 5.3 years ago by ▴ 10
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0
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1.0k
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Regarding hiding or removing the vertical line at center (at zero coordinate) average profile in Chipseeker
ChIPseeker
5.3 years ago Prasoon • 0
0
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1
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2.4k
views
How to use peak summits instead of TSS or transcript to plot heatmap for other factors
ChIPseqR ChIPs ChIPseeker ChIPSeq chipseq
updated 5.3 years ago by 68k • written 5.3 years ago by • 0
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0
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1.5k
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About metadata columns in Grange objects required for ChIPseeker analysis
ChIPseeker
5.4 years ago ahua217 ▴ 10
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0
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1.2k
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How to get the raw numbers of annotated features by ChIPseeker?
ChIPseeker
5.4 years ago bioinfouser2 ▴ 10
2
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1
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3.0k
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ChiPseeker package: plotAnnoPie identical colors for peakAnnoList features
ChiPseeker plotAnnoPie
5.5 years ago amafon95 ▴ 20
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1
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1.4k
views
p value after enrichPeakOverlap analysis in ChIPseeker
ChIPseeker
updated 2.6 years ago by • 0 • written 5.6 years ago by • 0
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0
replies
1.5k
views
ChIPseeker error when I wnat to get tagMatrix
Chipseeker TxDb getpromoters software error
5.8 years ago hfyuan2016 • 0
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0
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1.2k
views
Potential oversimplification in the overlap function
ChIPseeker
5.8 years ago konsta.kukkonen • 0
1
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0
replies
1.4k
views
Functional enrichment analysis issue/ChIPseeker package
ChIPseeker
5.8 years ago egbastakis • 0
0
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1
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2.3k
views
ChIPSeeker with Ensembl IDs
chipseeker Ensembl EnsDb.Mmusculus.v79 ensembldb
5.9 years ago Assa Yeroslaviz ★ 1.5k
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1
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1.5k
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ChIPSeeker - options(ChIPseeker.downstreamDistance = 500) seems not work
ChIPseeker
6.0 years ago Guandong Shang ▴ 40
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1
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2.2k
views
Using EnsDb.Hsapiens.v86 database doesn't fetch the ENSEMBL IDs
ChIPseeker
6.4 years ago sutturka • 0
1
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2
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4.5k
views
Unable to annotate the differential peaks from DiffBind using ChIPseeker
chip seq ChIPseeker peak annotation annotatePeak() Diffbind
6.5 years ago researcher • 0
2
votes
1
reply
5.2k
views
Finding the proper universe for enrichGO and enrichKEGG - only the genes that are annotated in those ontologies
chipseeker ChIPseeker
6.5 years ago endrebak85 ▴ 40
1
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3
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1.8k
views
Error: package or namespace load failed for 'ChIPseeker': 'TxDb.Hsapiens.UCSC.hg19.knownGene' is not exported from 'namespace: TxDb.Hsapiens.UCSC.hg1…
chipseq chipseeker R Bioconductor
updated 6.7 years ago by 25k • written 6.7 years ago by ▴ 20
0
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1
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3.6k
views
error in readPeakFile {chipseeker}
ChIPseeker readPeakFile
6.8 years ago Theo ▴ 10
0
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1
reply
1.6k
views
Problem in using covplot ChIPseeker
ChIPseeker software error
7.0 years ago vasudha.sharma • 0
3
votes
2
replies
2.6k
views
How to use EnsDb in annotatePeak from package "ChIPseeker"
GRanges ChIPseeker annotatePeak TxDb EnsDb
updated 7.0 years ago by ★ 2.1k • written 7.0 years ago by ▴ 100
1
vote
1
reply
2.4k
views
ChIPseeker genomicAnnotationPriority
annotation chipseeker
updated 4.6 years ago by • 0 • written 7.2 years ago by ▴ 10
0
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0
replies
1.6k
views
How to use ChIPseeker for getting genebody annotations.
chipseeker chipseq
7.2 years ago bioinfouser2 ▴ 10
0
votes
2
replies
1.7k
views
how to get frequencies from plotDistToTSS
chipseeker
7.2 years ago KKO • 0
97 results • Page 1 of 2
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Answer: GSEA error by James W. MacDonald 68k
At a very high level, the way non-model organisms are annotated is by using blast to find orthologs in other species that are well annotate…
Comment: Unable to find ENTREZ IDs by Adithi • 0
Hi James, Thank you so much for your reply. My main goal is to find ortholog genes from chinese hamster gene symbols to mouse gene symbols…
Comment: Unable to find ENTREZ IDs by Adithi • 0
Hi James, Thank you so much for your reply. My main goal is to find ortholog genes from chinese hamster gene symbols to mouse gene symbols…
Answer: Unable to find ENTREZ IDs by James W. MacDonald 68k
Those are the 'symbols', and are a concatenation of LOC and the NCBI Gene ID (what used to be called an Entrez Gene ID). As an example:http…
Answer: Inconsistencies between accessor functions for TxDb databases with selected seql by a2a2hd42aa • 0
Technical inconsistencies in database accessors can disrupt your workflow, but finding a reliable source to download online mobile games sh…
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Answer: OrgDb for maize
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Do I map probes to gene symbols BEFORE or AFTER differentially expressed gene analysis?
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